# HG changeset patch
# User peterjc
# Date 1416571363 18000
# Node ID 3070949d8fd7850037d0838742274bcb30c9cf0e
# Parent  93b8db68dde451034717d7cbdfb9fe1b39595cab
Uploaded v0.0.3, embedded citation

diff -r 93b8db68dde4 -r 3070949d8fd7 tools/samtools_idxstats/README.rst
--- a/tools/samtools_idxstats/README.rst	Wed Nov 13 07:05:15 2013 -0500
+++ b/tools/samtools_idxstats/README.rst	Fri Nov 21 07:02:43 2014 -0500
@@ -1,7 +1,7 @@
 Galaxy wrapper for samtools idxstats
 ====================================
 
-This wrapper is copyright 2013 by Peter Cock, The James Hutton Institute
+This wrapper is copyright 2013-2014 by Peter Cock, The James Hutton Institute
 (formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
 See the licence text below.
 
@@ -26,19 +26,19 @@
 To install the wrapper copy or move the following files under the Galaxy tools
 folder, e.g. in a ``tools/samtools_idxstats`` folder:
 
-* samtools_idxstats.xml (the Galaxy tool definition)
-* samtools_idxstats.py (the Python wrapper script)
-* README.rst (this file)
+* ``samtools_idxstats.xml`` (the Galaxy tool definition)
+* ``samtools_idxstats.py`` (the Python wrapper script)
+* ``README.rst`` (this file)
 
 You will also need to modify the ``tools_conf.xml`` file to tell Galaxy to offer
 the tool. Just add the line, perhaps under the NGS tools section::
 
   <tool file="samtools_idxstats/samtools_idxstats.xml" />
 
-If you wish to run the unit tests, also add this to tools_conf.xml.sample
-and move/copy the test-data files under Galaxy's test-data folder. Then::
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
 
-    $ ./run_functional_tests.sh -id samtools_idxstats
+    $ ./run_tests.sh -id samtools_idxstats
 
 That's it.
 
@@ -50,13 +50,15 @@
 Version Changes
 ------- ----------------------------------------------------------------------
 v0.0.1  - Initial public release
+v0.0.2  - Use quoted filenames when calling samtools (in case of spaces etc)
+v0.0.3  - Embed samtools citation in tool XML.
 ======= ======================================================================
 
 
 Developers
 ==========
 
-Development is one this GitHub repository:
+Development is on this GitHub repository:
 https://github.com/peterjc/pico_galaxy/tree/master/tools/samtools_idxstats
 
 For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
diff -r 93b8db68dde4 -r 3070949d8fd7 tools/samtools_idxstats/samtools_idxstats.py
--- a/tools/samtools_idxstats/samtools_idxstats.py	Wed Nov 13 07:05:15 2013 -0500
+++ b/tools/samtools_idxstats/samtools_idxstats.py	Fri Nov 21 07:02:43 2014 -0500
@@ -17,7 +17,7 @@
 
 if "-v" in sys.argv or "--version" in sys.argv:
     #Galaxy seems to invert the order of the two lines
-    print "(Galaxy wrapper v0.0.1)"
+    print "(Galaxy wrapper v0.0.2)"
     cmd = "samtools 2>&1 | grep -i ^Version"
     sys.exit(os.system(cmd))
 
@@ -49,7 +49,7 @@
 assert os.path.isfile(bam_file + ".bai"), bam_file
 
 #Run samtools idxstats:
-cmd = "samtools idxstats %s > %s" % (bam_file, tabular_filename)
+cmd = 'samtools idxstats "%s" > "%s"' % (bam_file, tabular_filename)
 return_code = os.system(cmd)
 
 #Remove the temp symlinks:
diff -r 93b8db68dde4 -r 3070949d8fd7 tools/samtools_idxstats/samtools_idxstats.xml
--- a/tools/samtools_idxstats/samtools_idxstats.xml	Wed Nov 13 07:05:15 2013 -0500
+++ b/tools/samtools_idxstats/samtools_idxstats.xml	Fri Nov 21 07:02:43 2014 -0500
@@ -1,4 +1,4 @@
-<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.1">
+<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.3">
     <description>samtools idxstats</description>
     <requirements>
         <requirement type="binary">samtools</requirement>
@@ -73,4 +73,7 @@
 This wrapper is available to install into other Galaxy Instances via the Galaxy
 Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
     </help>
+    <citations>
+        <citation type="doi">10.1093/bioinformatics/btp352</citation>
+    </citations>
 </tool>
diff -r 93b8db68dde4 -r 3070949d8fd7 tools/samtools_idxstats/tool_dependencies.xml
--- a/tools/samtools_idxstats/tool_dependencies.xml	Wed Nov 13 07:05:15 2013 -0500
+++ b/tools/samtools_idxstats/tool_dependencies.xml	Fri Nov 21 07:02:43 2014 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>